Examples with Dataset edu.harvard.iq.dataverse.Dataset used on opensource projects

Example 56 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class JsonParser method parseDataset.

public Dataset parseDataset(JsonObject obj) throws JsonParseException {
    Dataset dataset = new Dataset();
    dataset.setAuthority(obj.getString("authority", null) == null ? settingsService.getValueForKey(SettingsServiceBean.Key.Authority) : obj.getString("authority"));
    dataset.setProtocol(obj.getString("protocol", null) == null ? settingsService.getValueForKey(SettingsServiceBean.Key.Protocol) : obj.getString("protocol"));
    dataset.setDoiSeparator(obj.getString("doiSeparator", null) == null ? settingsService.getValueForKey(SettingsServiceBean.Key.DoiSeparator) : obj.getString("doiSeparator"));
    dataset.setIdentifier(obj.getString("identifier", null));
    DatasetVersion dsv = new DatasetVersion();
    dsv.setDataset(dataset);
    dsv = parseDatasetVersion(obj.getJsonObject("datasetVersion"), dsv);
    LinkedList<DatasetVersion> versions = new LinkedList<>();
    versions.add(dsv);
    dataset.setVersions(versions);
    return dataset;
}

Example 57 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class SolrIndexServiceBean method indexPermissionsOnSelfAndChildren.

/**
 * We use the database to determine direct children since there is no
 * inheritance
 */
public IndexResponse indexPermissionsOnSelfAndChildren(DvObject definitionPoint) {
    List<DvObject> dvObjectsToReindexPermissionsFor = new ArrayList<>();
    List<DataFile> filesToReindexAsBatch = new ArrayList<>();
    // so don't create a Solr "permission" doc either.
    if (definitionPoint.isInstanceofDataverse()) {
        Dataverse selfDataverse = (Dataverse) definitionPoint;
        if (!selfDataverse.equals(dataverseService.findRootDataverse())) {
            dvObjectsToReindexPermissionsFor.add(definitionPoint);
        }
        List<Dataset> directChildDatasetsOfDvDefPoint = datasetService.findByOwnerId(selfDataverse.getId());
        for (Dataset dataset : directChildDatasetsOfDvDefPoint) {
            dvObjectsToReindexPermissionsFor.add(dataset);
            for (DataFile datafile : filesToReIndexPermissionsFor(dataset)) {
                filesToReindexAsBatch.add(datafile);
            }
        }
    } else if (definitionPoint.isInstanceofDataset()) {
        // index the dataset itself
        indexPermissionsForOneDvObject(definitionPoint);
        dvObjectsToReindexPermissionsFor.add(definitionPoint);
        // index files
        Dataset dataset = (Dataset) definitionPoint;
        for (DataFile datafile : filesToReIndexPermissionsFor(dataset)) {
            filesToReindexAsBatch.add(datafile);
        }
    } else {
        dvObjectsToReindexPermissionsFor.add(definitionPoint);
    }
    /**
     * @todo Error handling? What to do with response?
     *
     * @todo Should update timestamps, probably, even thought these are
     * files, see https://github.com/IQSS/dataverse/issues/2421
     */
    String response = reindexFilesInBatches(filesToReindexAsBatch);
    List<String> updatePermissionTimeSuccessStatus = new ArrayList<>();
    for (DvObject dvObject : dvObjectsToReindexPermissionsFor) {
        /**
         * @todo do something with this response
         */
        IndexResponse indexResponse = indexPermissionsForOneDvObject(dvObject);
        DvObject managedDefinitionPoint = dvObjectService.updatePermissionIndexTime(definitionPoint);
        boolean updatePermissionTimeSuccessful = false;
        if (managedDefinitionPoint != null) {
            updatePermissionTimeSuccessful = true;
        }
        updatePermissionTimeSuccessStatus.add(dvObject + ":" + updatePermissionTimeSuccessful);
    }
    return new IndexResponse("Number of dvObject permissions indexed for " + definitionPoint + " (updatePermissionTimeSuccessful:" + updatePermissionTimeSuccessStatus + "): " + dvObjectsToReindexPermissionsFor.size());
}

Example 58 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class SolrIndexServiceBean method determineSolrDocsForFilesFromDataset.

private List<DvObjectSolrDoc> determineSolrDocsForFilesFromDataset(Map.Entry<Long, List<Long>> datasetHash) {
    List<DvObjectSolrDoc> emptyList = new ArrayList<>();
    List<DvObjectSolrDoc> solrDocs = emptyList;
    DvObject dvObject = dvObjectService.findDvObject(datasetHash.getKey());
    if (dvObject == null) {
        return emptyList;
    }
    if (dvObject.isInstanceofDataset()) {
        Dataset dataset = (Dataset) dvObject;
        solrDocs.addAll(constructDatafileSolrDocsFromDataset(dataset));
    }
    return solrDocs;
}

Example 59 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class SolrIndexServiceBean method reindexFilesInBatches.

private String reindexFilesInBatches(List<DataFile> filesToReindexPermissionsFor) {
    List<SolrInputDocument> docs = new ArrayList<>();
    Map<Long, List<Long>> byParentId = new HashMap<>();
    Map<Long, List<String>> permStringByDatasetVersion = new HashMap<>();
    for (DataFile file : filesToReindexPermissionsFor) {
        Dataset dataset = (Dataset) file.getOwner();
        Map<DatasetVersion.VersionState, Boolean> desiredCards = searchPermissionsService.getDesiredCards(dataset);
        for (DatasetVersion datasetVersionFileIsAttachedTo : datasetVersionsToBuildCardsFor(dataset)) {
            boolean cardShouldExist = desiredCards.get(datasetVersionFileIsAttachedTo.getVersionState());
            if (cardShouldExist) {
                List<String> cachedPermission = permStringByDatasetVersion.get(datasetVersionFileIsAttachedTo.getId());
                if (cachedPermission == null) {
                    logger.fine("no cached permission! Looking it up...");
                    List<DvObjectSolrDoc> fileSolrDocs = constructDatafileSolrDocs((DataFile) file, permStringByDatasetVersion);
                    for (DvObjectSolrDoc fileSolrDoc : fileSolrDocs) {
                        Long datasetVersionId = fileSolrDoc.getDatasetVersionId();
                        if (datasetVersionId != null) {
                            permStringByDatasetVersion.put(datasetVersionId, fileSolrDoc.getPermissions());
                            SolrInputDocument solrDoc = SearchUtil.createSolrDoc(fileSolrDoc);
                            docs.add(solrDoc);
                        }
                    }
                } else {
                    logger.fine("cached permission is " + cachedPermission);
                    List<DvObjectSolrDoc> fileSolrDocsBasedOnCachedPermissions = constructDatafileSolrDocs((DataFile) file, permStringByDatasetVersion);
                    for (DvObjectSolrDoc fileSolrDoc : fileSolrDocsBasedOnCachedPermissions) {
                        SolrInputDocument solrDoc = SearchUtil.createSolrDoc(fileSolrDoc);
                        docs.add(solrDoc);
                    }
                }
            }
        }
        Long parent = file.getOwner().getId();
        List<Long> existingList = byParentId.get(parent);
        if (existingList == null) {
            List<Long> empty = new ArrayList<>();
            byParentId.put(parent, empty);
        } else {
            List<Long> updatedList = existingList;
            updatedList.add(file.getId());
            byParentId.put(parent, updatedList);
        }
    }
    try {
        persistToSolr(docs);
        return " " + filesToReindexPermissionsFor.size() + " files indexed across " + docs.size() + " Solr documents ";
    } catch (SolrServerException | IOException ex) {
        return " tried to reindex " + filesToReindexPermissionsFor.size() + " files indexed across " + docs.size() + " Solr documents but caught exception: " + ex;
    }
}

Example 60 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class AddReplaceFileHelper method step_070_run_update_dataset_command.

/**
 * Create and run the update dataset command
 *
 * @return
 */
private boolean step_070_run_update_dataset_command() {
    if (this.hasError()) {
        return false;
    }
    Command<Dataset> update_cmd;
    update_cmd = new UpdateDatasetCommand(dataset, dvRequest);
    ((UpdateDatasetCommand) update_cmd).setValidateLenient(true);
    try {
        // Submit the update dataset command
        // and update the local dataset object
        // 
        dataset = commandEngine.submit(update_cmd);
    } catch (CommandException ex) {
        /**
         * @todo Add a test to exercise this error.
         */
        this.addErrorSevere(getBundleErr("add.add_file_error"));
        logger.severe(ex.getMessage());
        return false;
    } catch (EJBException ex) {
        /**
         * @todo Add a test to exercise this error.
         */
        this.addErrorSevere("add.add_file_error (see logs)");
        logger.severe(ex.getMessage());
        return false;
    }
    return true;
}